Extreme environmental conditions such as those found in the polar regions on Earth are thought to explore the limits of life and the strategies evolved by microorganisms to adapt to extreme environments. The high Arctic has been long considered a suitable terrestrial analogue to Mars in many geological and astrobiological aspects. We used a combination of pyro-sequencing and microscopy methods to examine endolithic microbial communities on five different rock types (sandstone, limestone, basalt, granite, and travertine). Bacterial communities showed slight variation between different rock types. Bacterial communities were dominated by Actinobacteria, Proteobacteria, Chloroflexi, Bacteroidetes, and Acidobacteria. Blast result revealed that dominant endolithic OTUs in this environment are highly affiliated with those found in soils or rocks of Arctic and Antarctica, suggesting ‘niche conservatism’ occurs at a global scale. Mantel test was performed to further explore the correlations between endolithic microbial community and chemical composition of rocks, and showed significant positive correlations between bacterial communities and most of the major elements including Si, Al, Fe, Mg, P, K, and Ti. This study shows that endolithic communities are associated with the type of rock and its localities.